"F*** Yourselves" read the graffiti scrawled in blue letters on the facade of the house, according to photographs published in the German press on Tuesday.
"One can say it is connected" with the worldwide child sex abuse scandal, a police spokesman said.
The 30-centimetre (12-inch) high letters of the slogan, first noticed at 6.45am (1445 AEST) on Tuesday, were hastily painted over.
Police have appealed for witnesses.
The damage to the house, a three-storey, 264-year-old building on the market square in the picturesque village of Marktl am Inn on the Austrian border, was estimated at 1,500 euros ($A2,162), police said.
The house, where the then Joseph Ratzinger was born in 1927, has become a pilgrimage site for Catholics from around the world.
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